Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
Human induced Pluripotent Stem Cells
cell type
Human induced Pluripotent Stem Cells
antibody
Abcam ab8580 (Rabbit polyclonal anti-Histone H3 (tri-methyl K4))

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were subjected to cross-linking. After fixation with 1% formamide, cells were sonicated to shear DNA. DNA-protein complexes were incubated with Protein G beads (GE Healthcare) and anti-histone modification polyclonal antibodies (H3K4me1/H3K4me3/H3K27ac/H3K36me3). After washing the beads, immunoprecipitants were eluted with 30 µL of Tris buffer. Multiplexed ChIP-seq libraries were prepared from 10 ng of immunoprecipitated DNA fragments using NEBNext ChIP-seq Library Prep Master Mix (New England BioLabs). For sequencing using GAIIx (Illumina), cluster generation was performed using TruSeq SR Cluster Kit v2 (Illumina). Each lane of flow cells contained one sample. Sequencing was performed in single-read run mode with a total 76 cycles, including a 75-bp read and one cycle for phasing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
37278476
Reads aligned (%)
67.5
Duplicates removed (%)
9.1
Number of peaks
22231 (qval < 1E-05)

hg19

Number of total reads
37278476
Reads aligned (%)
67.0
Duplicates removed (%)
10.0
Number of peaks
22137 (qval < 1E-05)

Base call quality data from DBCLS SRA